World Microbiome Day: Open access HoloFood Data Portal can help create more sustainable animal feeds

27 Jun 2023 --- After scrutinizing the interplay between the diets of chicken and salmon and its effects on their complex microbiomes for four years, the HoloFood project, in partnership with the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI), are launching the HoloFood Data Portal.

The portal is free to access and use and makes all of the project’s findings available to producers looking to create better feeds and maximize meat production. Supported by Horizon 2020 and developed by EMBL-EBI, the portal aims to pave the way for sustainable animal feeds.

“Building on EMBL-EBI’s 30 years of expertise in managing the world’s biological data, the HoloFood Data Portal makes all the data collected by the project freely-accessible to researchers worldwide,” Dr. Rob Finn, team leader at EMBL-EBI, tells Nutrition Insight.

“They can use the data to explore the relationships between the animal, the microbes living in its gut and what the animal is fed, in order to develop improved, more sustainable feed options.” 

Promoting sustainable animal feeds
Animal agriculture, an industry often maligned for its resource-intensive practices, has long sought ways to mitigate its environmental impact while ensuring food security. By zeroing in on the chicken and salmon species, the HoloFood project states it has identified promising substitutes.Dr. Rob Finn, team leader at EMBL-EBI.

“A key insight from the HoloFood project is that blue mussels appear to be a sustainable alternative for salmon feed,” explains Finn. “At the moment, a large proportion of farmed salmon are fed fish meal. This means that wild-caught anchovies and herring, for example, are being used to feed farmed salmon.” 

“This is not sustainable and has already contributed to the collapse of fish populations. HoloFood found that blue mussels, which are very common and easy to cultivate, could serve as a more sustainable alternative, without affecting salmon health and meat quality.”

An “empowering” tool
HoloFood underscores that the data portal is the first freely accessible database of its kind, providing researchers with unprecedented access to comprehensive information on the microbial diversity within the microbiome of chickens and salmon. 

Moreover, the dataset enables researchers to examine how changes in diet impact animal health.

“There are no restrictions on accessing and using the HoloFood data,” Finn stresses. “This builds on EMBL-EBI’s open data approach, which champions making research data open to all. It is providing useful analysis tools and empowers other scientists around the world to pursue their own research questions relevant to their social and cultural contexts, develop complementary experiments and push the boundaries of knowledge even further.”

“Working in isolation can only get us so far – we need to work together and one way to do this is by making scientific results and data openly available. This will help us speed up the pace of discovery and develop practical solutions to urgent, global challenges, such as food security.” 

Unlocking the animal microbiome
According to the project, the core of these innovative scientific concepts is hologenomics. Finn explains that a hologenome consists of all the genomes that make up an individual organism, including the host and the microbes that live symbiotically with it. 

By treating the host animal and its interacting microorganisms as a unified entity, known as a holobiont, the project amassed a wealth of information about chicken and salmon, including host animal genomes, metagenomes, metabolomes and phenotypic data. 

The dataset will allow researchers to explore the influence of different feed types on crucial factors such as microbiome composition, growth, immune response and meat quality.The portal can be used freely to help producers make more sustainable salmon and chicken feed offerings. Image Credit: HoloFood Data Portal

“For example, we know that gut microbes in chickens can be manipulated through the use of feed additives such as prebiotics and probiotics,” Finn elaborates. “However, the microbial responses to feed additives might differ depending on the genetic background and developmental stage of the chicken, as well as the farming environment.”

“By analyzing the chicken and the microbes living in and around it as a single unit, researchers can start to decipher the biomolecular and physiological processes triggered by incorporating feed additives and novel sustainable feeds in farmed animals.”

Setting the research bar higher
HoloFood states that central to the Data Portal’s significance is its role as a catalyst for global collaboration and knowledge sharing. By providing open access to the dataset, researchers worldwide can embark on in-depth investigations and gain novel insights into sustainable animal feed development.

Furthermore, it holds that the portal’s value lies not only in the depth and breadth of the available data but also in its interconnectedness. The curated and annotated information can serve as a foundation for developing new tools and algorithms to promote understanding of organisms within their environments. 

“HoloFood showed that collecting, analyzing and sharing this kind of data set is feasible,” Finn concludes. “The next step is to generate more of these data sets, develop data analysis tools for untangling host-microbiome interactions in multi-omic data sets and to validate these tools against commercially-relevant test cases for more sustainable food production.”

By William Bradford Nichols